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- PDB-6u0a: Human Angiopoietin-Like 4 C-Terminal Domain (cANGPTL4) with Glycerol -

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Basic information

Entry
Database: PDB / ID: 6u0a
TitleHuman Angiopoietin-Like 4 C-Terminal Domain (cANGPTL4) with Glycerol
ComponentsAngiopoietin-related protein 4
KeywordsSIGNALING PROTEIN / Fibrinogen-like domain / Angiogenesis / Cancer cells / Metastasis
Function / homology
Function and homology information


regulation of chylomicron remodeling / lipase inhibitor activity / lipase binding / Assembly of active LPL and LIPC lipase complexes / Regulation of CDH11 function / negative regulation of very-low-density lipoprotein particle remodeling / negative regulation of fatty acid biosynthetic process / endothelial cell apoptotic process / triglyceride homeostasis / protein unfolding ...regulation of chylomicron remodeling / lipase inhibitor activity / lipase binding / Assembly of active LPL and LIPC lipase complexes / Regulation of CDH11 function / negative regulation of very-low-density lipoprotein particle remodeling / negative regulation of fatty acid biosynthetic process / endothelial cell apoptotic process / triglyceride homeostasis / protein unfolding / enzyme inhibitor activity / negative regulation of endothelial cell apoptotic process / PPARA activates gene expression / Transcriptional regulation of white adipocyte differentiation / lipid metabolic process / positive regulation of angiogenesis / blood coagulation / : / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / angiogenesis / blood microparticle / response to hypoxia / negative regulation of apoptotic process / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 ...Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Angiopoietin-related protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsTarver, C.L. / Yuan, Q. / Singhal, A.J. / Ramaker, R. / Cooper, S. / Pusey, M.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)5R42GM116283-03 United States
CitationJournal: To Be Published
Title: Crystal Structures of Angiopoietin-Like 4 C-Terminal Domain (cANGPTL4) Reveal a Binding Pocket with Multiple Ligands
Authors: Tarver, C.L. / Yuan, Q. / Singhal, A.J. / Ramaker, R. / Cooper, S. / Pusey, M.L.
History
DepositionAug 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Angiopoietin-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5502
Polymers24,4581
Non-polymers921
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.489, 134.868, 39.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Angiopoietin-related protein 4 / Angiopoietin-like protein 4 / Hepatic fibrinogen/angiopoietin-related protein / HFARP


Mass: 24458.404 Da / Num. of mol.: 1 / Fragment: C-Terminal Domain, residues 185-400
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ANGPTL4, ARP4, HFARP, PGAR, PP1158, PSEC0166, UNQ171/PRO197
Plasmid: pET3a / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): T7 SHuffle / Variant (production host): Resistance to phage T1 (fhuA2) / References: UniProt: Q9BY76
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.1 M HEPES 7.5, 0.1 M sodium chloride, and 1.6 M ammonium sulfate This solution with 20% glycerol was used as a cryoprotectant
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.11→47.44 Å / Num. obs: 20254 / % possible obs: 98.31 % / Redundancy: 6.3 % / Biso Wilson estimate: 37.31 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.036 / Rrim(I) all: 0.091 / Net I/σ(I): 13.5
Reflection shellResolution: 2.11→2.15 Å / Redundancy: 6 % / Rmerge(I) obs: 0.639 / Num. unique obs: 922 / CC1/2: 0.827 / Rpim(I) all: 0.28 / Rrim(I) all: 0.7 / % possible all: 99.2

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Processing

Software
NameClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z3S

1z3s


Resolution: 2.11→47.16 Å / SU ML: 0.2073 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.9253
RfactorNum. reflection% reflection
Rfree0.2369 1924 9.5 %
Rwork0.2138 --
obs0.2159 20254 95.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.12 Å2
Refinement stepCycle: LAST / Resolution: 2.11→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 6 49 1781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621783
X-RAY DIFFRACTIONf_angle_d1.0312416
X-RAY DIFFRACTIONf_chiral_restr0.0571241
X-RAY DIFFRACTIONf_plane_restr0.0054317
X-RAY DIFFRACTIONf_dihedral_angle_d21.0048653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.160.29881250.25931167X-RAY DIFFRACTION88.74
2.16-2.220.2971310.24241213X-RAY DIFFRACTION88.95
2.22-2.280.29761250.24821244X-RAY DIFFRACTION92.06
2.28-2.360.26891310.21951235X-RAY DIFFRACTION92.67
2.36-2.440.29011400.22771266X-RAY DIFFRACTION93.61
2.44-2.540.23481320.21961275X-RAY DIFFRACTION94.68
2.54-2.650.25621350.21481304X-RAY DIFFRACTION95.55
2.65-2.790.23411400.21281321X-RAY DIFFRACTION96.63
2.79-2.970.22931360.20081334X-RAY DIFFRACTION98.13
2.97-3.20.2221440.20371346X-RAY DIFFRACTION98.94
3.2-3.520.2291390.20511384X-RAY DIFFRACTION99.15
3.52-4.030.20411440.19681370X-RAY DIFFRACTION99.41
4.03-5.080.2141480.19411400X-RAY DIFFRACTION99.29
5.08-47.160.25931540.24431471X-RAY DIFFRACTION98.78

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